Hello DAC,
I downloaded AmberTools-1.5.tar.bz2 from
http://ambermd.org/AmberTools-get.html, but I don't remember how to get bug fix.all. Whenever I clicked "bugfix.all", I was led to the webpage, and I did not know how to download from there.
As you suspected I got the html version, I just copied the webpage into an emacs file and saved as "bugfix.all" in $AMBERHOME. % patch -p0 -N <bugfix.all" seemed fine.
% sudo ./configure -macAccelerate -nopython gnu had no more error.
However, % sudo make install >temp2produced the errors attached below.
The temp2 file contained only the following line related to "error":% grep -n error temp230: /usr/bin/install -c -m 644 error.h errorHandler.h '/Users/genzotanaka/Downloads/amber11/include/mtkpp/Log'
I would appreciate if you could give me advice.
Thanks
Genzo
.........................
sudo make >temp2Password:ranlib: file: /Users/genzotanaka/Downloads/amber11/lib/libtinyxml.a(tinystr.o) has no symbolsar: creating archive arpack.a./py_setup.sh: line 6: dirname/Users/genzotanaka/Downloads/amber11: No such file or directoryar: creating archive arpack.aar: creating archive arpack.aar: creating archive libpdb.aar: creating archive arpack.aparmSet.c: In function ‘iParmSetAddProperTerm’:parmSet.c:1610: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:1610: error: ‘dScee’ undeclared (first use in this function)parmSet.c:1610: error: (Each undeclared identifier is reported only onceparmSet.c:1610: error: for each function it appears in.)parmSet.c:1611: error: ‘TORSIONPARMt’ has no member named ‘dScnb’parmSet.c:1611: error: ‘dScnb’ undeclared (first use in this function)parmSet.c: In function ‘ParmSetTORSIONTerm’:parmSet.c:2042: error: ‘dPScee’ undeclared (first use in this function)parmSet.c:2042: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:2043: error: ‘dPScnb’ undeclared (first use in this function)parmSet.c:2043: error: ‘TORSIONPARMt’ has no member named ‘dScnb’parmSet.c: In function ‘bParmSetTORSIONAddProperTerm’:parmSet.c:2075: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:2075: error: ‘dScee’ undeclared (first use in this function)parmSet.c:2076: error: ‘TORSIONPARMt’ has no member named ‘dScnb’parmSet.c:2076: error: ‘dScnb’ undeclared (first use in this function)parmSet.c: In function ‘bParmSetTORSIONAddImproperTerm’:parmSet.c:2115: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:2115: error: ‘dScee’ undeclared (first use in this function)parmSet.c:2116: error: ‘TORSIONPARMt’ has no member named ‘dScnb’parmSet.c:2116: error: ‘dScnb’ undeclared (first use in this function)parmSet.c: In function ‘ParmSetTorsion’:parmSet.c:2556: error: ‘dPScee’ undeclared (first use in this function)parmSet.c:2556: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:2557: error: ‘dPScnb’ undeclared (first use in this function)parmSet.c:2557: error: ‘TORSIONPARMt’ has no member named ‘dScnb’parmSet.c: In function ‘ParmSetImproper’:parmSet.c:2600: error: ‘dPScee’ undeclared (first use in this function)parmSet.c:2600: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:2601: error: ‘dPScnb’ undeclared (first use in this function)parmSet.c:2601: error: ‘TORSIONPARMt’ has no member named ‘dScnb’parmSet.c: In function ‘ParmSetUpdateTorsion’:parmSet.c:2772: error: ‘dPScee’ undeclared (first use in this function)parmSet.c:2772: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:2773: error: ‘dPScnb’ undeclared (first use in this function)parmSet.c:2773: error: ‘TORSIONPARMt’ has no member named ‘dScnb’parmSet.c: In function ‘ParmSetUpdateImproper’:parmSet.c:2810: error: ‘dPScee’ undeclared (first use in this function)parmSet.c:2810: error: ‘TORSIONPARMt’ has no member named ‘dScee’parmSet.c:2811: error: ‘dPScnb’ undeclared (first use in this function)parmSet.c:2811: error: ‘TORSIONPARMt’ has no member named ‘dScnb’make[2]: *** [parmSet.o] Error 1make[1]: *** [install] Error 2make: *** [serial] Error 2
> Date: Mon, 2 Apr 2012 08:19:13 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] AmberTools-1.5 installation problems
>
> On Mon, Apr 02, 2012, Genzo Tanaka wrote:
> >
> > % sudo ./configure -macAccelerate -nopython gnu
> > seemed fine, but with 2 errors:
> > ./configure: line 2169: syntax error near unexpected token `&'
> > ./configure: line 2169: ` ../../AT15_Amber11.py > Amber11_Conversion.log 2>&1'
> >
>
> It looks like somehow you have html codes (like ">") instead of the real
> characters (in this case, ">") in your files. I'm not sure how this could
> have happened: how did you obtain the files?
>
> > stdGroup.cpp: In member function 'double MTKpp::stdGroup::getCharge()':
> > stdGroup.cpp:271: error: missing template arguments before '&' token
> > stdGroup.cpp:271: error: 'lt' was not declared in this scope
> > stdGroup.cpp:271: error: 'gt' declared as reference but not initialized
>
> This looks like the same kind of problem: instead of ">" and "<" characters,
> you have their html equivalents.
>
> ....dac
>
>
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Received on Mon Apr 02 2012 - 15:00:03 PDT
